Introduction

In genome assembly, as coverage of sequencing and genome size growing, most current softwares require a large memory for handling a great deal of sequence data. However, most researchers usually cannot meet the requirements of computing resources which prevent most current softwares from practical applications.In this article, we present an update algorithm called EPGA2, which applies some new modules and can bring about improved assembly results in small memory. For reducing peak memory in genome assembly, EPGA2 adopts memory-efficient DSK to count K-mers and revised BCALM to construct De Bruijn Graph. Moreover, EPGA2 parallels the step of Contigs Merging and adds Errors Correction in its pipeline. Our experiments demonstrate that all these changes in EPGA2 are more useful for genome assembly.EPGA2 is publicly available for download at https://github.com/bioinfomaticsCSU/EPGA2.

Publications

  1. EPGA2: memory-efficient de novo assembler.
    Cite this
    Luo J, Wang J, Li W, Zhang Z, Wu FX, Li M, Pan Y, 2015-12-01 - Bioinformatics (Oxford, England)
  2. EPGA: de novo assembly using the distributions of reads and insert size.
    Cite this
    Luo J, Wang J, Zhang Z, Wu FX, Li M, Pan Y, 2015-03-01 - Bioinformatics (Oxford, England)

Credits

  1. Junwei Luo
    Developer

    School of Information Science and Engineering, Central South University, China

  2. Jianxin Wang
    Developer

    School of Information Science and Engineering, Central South University, China

  3. Weilong Li
    Developer

    School of Information Science and Engineering, Central South University, China

  4. Zhen Zhang
    Developer

    School of Information Science and Engineering, Central South University, China

  5. Fang-Xiang Wu
    Developer

    Division of Biomedical Engineering, University of Saskatchewan, Canada

  6. Min Li
    Developer

    School of Information Science and Engineering, Central South University, China

  7. Yi Pan
    Investigator

    Department of Computer Science, Georgia State University, United States of America

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Summary
AccessionBT002213
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++
User InterfaceTerminal Command Line
Download Count0
Country/RegionUnited States of America
Submitted ByYi Pan